From 20d988ff35e8430300859cc8c55ff82c6d76c13c Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Thu, 4 Feb 2021 15:49:44 -0500
Subject: [PATCH] Update owl-diff version.

---
 robot-core/pom.xml                            |  2 +-
 .../org/obolibrary/robot/RenameOperation.java |  7 ++---
 .../robot/metrics/MetricsUtils.java           | 31 +++++++++----------
 3 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/robot-core/pom.xml b/robot-core/pom.xml
index 3bdfad0c8..dcbfd0ed9 100644
--- a/robot-core/pom.xml
+++ b/robot-core/pom.xml
@@ -170,7 +170,7 @@
     <dependency>
       <groupId>org.geneontology</groupId>
       <artifactId>owl-diff_${scala.version}</artifactId>
-      <version>1.2.1</version>
+      <version>1.2.2</version>
     </dependency>
     <dependency>
       <groupId>org.geneontology</groupId>
diff --git a/robot-core/src/main/java/org/obolibrary/robot/RenameOperation.java b/robot-core/src/main/java/org/obolibrary/robot/RenameOperation.java
index d29834efc..e7e5fb750 100644
--- a/robot-core/src/main/java/org/obolibrary/robot/RenameOperation.java
+++ b/robot-core/src/main/java/org/obolibrary/robot/RenameOperation.java
@@ -71,11 +71,8 @@ public static void renameFull(
    * @throws Exception if the old IRI in a mapping does not exist
    */
   public static void renameFull(
-    OWLOntology ontology,
-    IOHelper ioHelper,
-    Map<String, String> mappings)
-    throws Exception {
-    renameFull(ontology,ioHelper,mappings,false);
+      OWLOntology ontology, IOHelper ioHelper, Map<String, String> mappings) throws Exception {
+    renameFull(ontology, ioHelper, mappings, false);
   }
 
   /**
diff --git a/robot-core/src/main/java/org/obolibrary/robot/metrics/MetricsUtils.java b/robot-core/src/main/java/org/obolibrary/robot/metrics/MetricsUtils.java
index ba00c43a9..b042ea567 100644
--- a/robot-core/src/main/java/org/obolibrary/robot/metrics/MetricsUtils.java
+++ b/robot-core/src/main/java/org/obolibrary/robot/metrics/MetricsUtils.java
@@ -1,15 +1,14 @@
 package org.obolibrary.robot.metrics;
 
+import java.util.HashSet;
+import java.util.Set;
 import org.semanticweb.owlapi.model.AxiomType;
 import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.parameters.Imports;
 
-import java.util.HashSet;
-import java.util.Set;
-
-//@SuppressWarnings("unused")
+// @SuppressWarnings("unused")
 public class MetricsUtils {
 
   /**
@@ -28,17 +27,17 @@ public static Set<OWLAxiom> getABoxAxioms(Set<OWLAxiom> axioms) {
   }
 
   /**
-   * @param ontology              ontology to be checked
+   * @param ontology ontology to be checked
    * @param includeImportsClosure take into account imports
-   * @param skiprules             ignore rules (SWRL)
-   * @param types                 AxiomTypes to consider
+   * @param skiprules ignore rules (SWRL)
+   * @param types AxiomTypes to consider
    * @return all logical axioms in the ontology
    */
   public static Set<OWLAxiom> getLogicalAxioms(
-    OWLOntology ontology,
-    Imports includeImportsClosure,
-    boolean skiprules,
-    Set<AxiomType<?>> types) {
+      OWLOntology ontology,
+      Imports includeImportsClosure,
+      boolean skiprules,
+      Set<AxiomType<?>> types) {
     return getLogicalAxioms(ontology, includeImportsClosure, skiprules, false, types);
   }
 
@@ -82,11 +81,11 @@ private static Set<OWLAxiom> stripAnnotations(Set<OWLAxiom> axioms) {
   }
 
   private static Set<OWLAxiom> getLogicalAxioms(
-    OWLOntology ontology,
-    Imports includeImportsClosure,
-    boolean skiprules,
-    @SuppressWarnings("SameParameterValue") boolean stripaxiomanno,
-    Set<AxiomType<?>> types) {
+      OWLOntology ontology,
+      Imports includeImportsClosure,
+      boolean skiprules,
+      @SuppressWarnings("SameParameterValue") boolean stripaxiomanno,
+      Set<AxiomType<?>> types) {
     Set<OWLAxiom> axioms = new HashSet<>();
     for (OWLAxiom ax : ontology.getLogicalAxioms()) {
       if (types.contains(ax.getAxiomType())) {

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